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b/stay_admission/admission_downstream.py |
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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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import json |
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import pickle |
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import pandas as pd |
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import numpy as np |
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import sparse |
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import torch |
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import model |
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from tqdm import tqdm |
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from torch import nn, optim |
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from torch.utils.data import DataLoader |
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import torch.nn.functional as F |
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import sklearn |
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from sklearn.metrics import classification_report, roc_auc_score, average_precision_score, cohen_kappa_score, f1_score |
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import matplotlib.pyplot as plt |
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from baseline import * |
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from operations import * |
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from train import * |
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from model import * |
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import sys |
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import csv |
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import os |
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print(sys.argv[2:]) |
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EPOCHS,LR, BATCH, SEED, TASK, DEVICE = sys.argv[2:] |
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EPOCHS,LR, BATCH, SEED, TASK, DEVICE = int(EPOCHS), float(LR), int(BATCH), int(SEED), str(TASK), str(DEVICE) |
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PATH = "hmp_results/" + TASK + '/' |
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if str(EPOCHS) + '_' + str(LR) + '_' + str(BATCH)+ '_' +'.csv' in os.listdir(PATH): |
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print("conducted experiments") |
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else: |
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device = torch.device(DEVICE) |
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data = pickle.load(open("data/hmp_admission.p", 'rb')) |
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split_mark = int(len(data)*0.8), int(len(data)*0.9) |
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def collate_batch(batch_data): |
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icd = torch.tensor([i[0] for i in batch_data]).to(torch.float32).to(device) |
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drug = torch.tensor([i[1] for i in batch_data]).to(torch.float32).to(device) |
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X = torch.tensor(np.array([np.stack(i[2], axis = 0) for i in batch_data])).to(torch.float32).to(device) |
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S = torch.tensor(np.array([np.stack(i[3], axis = 0) for i in batch_data])).to(torch.float32).to(device) |
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input_ids = torch.stack([i[4] for i in batch_data]).to(device) |
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attention_mask = torch.stack([i[5] for i in batch_data]).to(device) |
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token_type_ids = torch.stack([i[6] for i in batch_data]).to(device) |
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label = torch.tensor(np.array([i[-1] for i in batch_data])).to(torch.float32).to(device) |
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return [icd , drug, X, S, input_ids, attention_mask, token_type_ids, label] |
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def collate_batch_ts(batch_data): |
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X = torch.tensor(np.array([i[0] for i in batch_data])).to(torch.float32).to(device) |
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label = torch.tensor(np.array([i[4] for i in batch_data])).to(torch.float32).to(device) |
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return [X, label] |
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# multimodal encoder evaluation |
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test = DataLoader(data[split_mark[1]:], batch_size = BATCH, shuffle = True, collate_fn=collate_batch) |
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train = DataLoader(data[:split_mark[0]], batch_size = BATCH, shuffle = True, collate_fn=collate_batch) |
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valid = DataLoader(data[split_mark[0]:split_mark[1]], batch_size = BATCH, shuffle = True, collate_fn=collate_batch) |
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MedHMP = HADM_CLS(7686+1, 1701+1, 256, 0.8).to(device) |
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MedHMP.train() |
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enc = torch.load("model/admission_pretrained.p").state_dict() |
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model_dict = MedHMP.state_dict() |
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state_dict = {k.split('enc.')[-1]:v for k,v in enc.items() if k.split('enc.')[-1] in model_dict.keys()} |
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MedHMP.state_dict().update(state_dict) |
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MedHMP.load_state_dict(state_dict, strict = False) |
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MedHMP, _ = adm_trainer(MedHMP, train, valid, test,EPOCHS, LR, BATCH, SEED, device , encoder = 'HMP', patience = 5) |
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file = open(PATH +str(EPOCHS) + '_' + str(LR) + '_' + str(BATCH)+ '_' +'.csv','w',encoding = 'gbk') |
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csv_w = csv.writer(file) |
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metrics = list(eval_metric_admission(test, MedHMP, device, 'HMP'))[:-1] |
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csv_w.writerow(["MedHMP"] + metrics) |
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file.close() |
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globals().clear() |
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